Proteogenomic analysis of bradyrhizobium japonicum USDA110 using genosuite, an automated multi-algorithmic pipeline

Kumar, Dhirendra, Yadav, Amit Kumar, Kadimi, Puneet Kumar, Nagaraj, Shivashankar H., Grimmond, Sean M. and Dash, Debasis (2013) Proteogenomic analysis of bradyrhizobium japonicum USDA110 using genosuite, an automated multi-algorithmic pipeline. Molecular and Cellular Proteomics, 12 11: 3388-3397. doi:10.1074/mcp.M112.027169


Author Kumar, Dhirendra
Yadav, Amit Kumar
Kadimi, Puneet Kumar
Nagaraj, Shivashankar H.
Grimmond, Sean M.
Dash, Debasis
Title Proteogenomic analysis of bradyrhizobium japonicum USDA110 using genosuite, an automated multi-algorithmic pipeline
Journal name Molecular and Cellular Proteomics   Check publisher's open access policy
ISSN 1535-9476
1535-9484
Publication date 2013-01-01
Year available 2013
Sub-type Article (original research)
DOI 10.1074/mcp.M112.027169
Volume 12
Issue 11
Start page 3388
End page 3397
Total pages 10
Place of publication Bethesda, MD, United States
Publisher American Society for Biochemistry and Molecular Biology
Language eng
Subject 1303 Specialist Studies in Education
1312 Molecular Biology
1602 Criminology
Abstract We present GenoSuite, an integrated proteogenomic pipeline to validate, refine and discover protein coding genes using high-throughput mass spectrometry (MS) data from prokaryotes. To demonstrate the effectiveness of GenoSuite, we analyzed proteomics data of Bradyrhizobium japonicum (USDA110), a model organism to study agriculturally important rhizobium-legume symbiosis. Our analysis confirmed 31% of known genes, refined 49 gene models for their translation initiation site (TIS) and discovered 59 novel protein coding genes. Notably, a novel protein which redefined the boundary of a crucial cytochrome P450 system related operon was discovered, known to be highly expressed in the anaerobic symbiotic bacteroids. A focused analysis on N-terminally acetylated peptides indicated downstream TIS for gene blr0594. Finally, ortho-proteogenomic analysis revealed three novel genes in recently sequenced B. japonicum USDA6T genome. The discovery of large number of missing genes and correction of gene models have expanded the proteomic landscape of B. japonicum and presents an unparalleled utility of proteogenomic analyses and versatility of GenoSuite for annotating prokaryotic genomes including pathogens.
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ
Additional Notes First published on: 23 July 2013.

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2014 Collection
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